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Molecular Interactions

Molecular Interactions are crucial for a function of biological system, there are wide range of interactions. Our group mainly focussed on prediction of molecules interacting residues in a protein. Broadly, these servers predict; i) glycosylation sites, ii) small molecules (e.g., ATP, GTP) interacting sites, iii)nucleotide binding sites and iv) protein-protein interaction.

Predicting Interaction between biomolecules (Raghava's Group)

  1. ADPint:Predicion of ADP interacting residue.
  2. ATPint: Identification of ATP binding sites in ATP-binding proteins.
  3. CRIP: Computational Resources for molecular Interaction Prediction
  4. DNAint: Prediction of DNA Interacting Residues.
  5. GlycoEP: Prediction of C-, N- and O-glycosylation site in eukaryotic proteins. 
  6. GlycoPP: Prediction of potential N-and O-glycosites in prokaryotic proteins.
  7. GTPbinder: Identification of GTP binding residue in protein sequences. 
  8. HIVint: Prediction of protein-protein interaction between HIV and Human proteins.
  9. LPIcom: Analysis and prediction of ligand protein interaction.
  10. NADbinder: Prediction of NAD interacting residues in proteins.
  11. NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence
  12. PAAINT: A webservice for predicting residue-residue contacts in proteins.
  13. PPDBench:  Benchmarking of docking software on protein-peptide complexes.
  14. Pprint:  A  web-server for predicting RNA-binding residues of a protein.
  15. PreMieR:  A webserver for the prediction of Mannose Interacting residue.
  16. ProPrInt: A web-server predicts physical or functional interactions between protein molecules.
  17. RISICbinder: Prediction of guide strand of microRNAs from its sequence and secondary structure.
  18. RNAint: Identification of RNA interacting residues in a protein.
  19. RNApin: Prediction of Protein Interacting Nucleotides (PINs) in RNA sequences.
  20. RNApred: A webserver for the prediction of RNA binding proteins.
  21. RRCpred: A Webserver for predicting residue-residue contact.
  22. SAMbinder: Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
  23. VitaPred: A webserver for predicting the vitamin interacting residue.

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein:ligand complex.
  2. COILCHECK: an interactive server for the analysis of interface regions in coiled coils.
  3. DenHunt : A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.
  4. DRGAS: a database of functional genetic variants and their phosphorylation states in human DNA repair systems.
  5. ECMIS: computational approach for the identification of hotspots at protein:protein interfaces.
  6. EnPPIpred: Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study.
  7. HADDOCK: Describes the modelling and interaction of bio-molecular complexes such as protein-protein, protein-DNA
  8. HORI: a web server to compute Higher Order Residue Interactions in protein structures.
  9. Hu-Vir: Molecular principles of human virus protein-protein interactions.
  10. MolSurfer:  A Macromolecular Interface Navigator.
  11. PathBLAST: "Search protein-protein interaction network of any selected organism and extracts all interaction pathways "
  12. PLIC: protein:ligand interaction clusters.
  13. PPIMpred: A web server for high-throughput screening of small molecules targeting protein-protein interaction.
  14. PRDBv2: A non-redundant protein-RNA docking benchmark version 2.0.
  15. SigMol: Repertoire of quorum sensing signaling molecules in prokaryotes.
  16. SPEER-SERVER: a web server for prediction of protein specificity determining sites.